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(-)Makefile (-3 / +3 lines)
Lines 1-8 Link Here
1 
# $FreeBSD$
 1 
# $FreeBSD$
2 

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          3
          
PORTNAME=	blast+

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PORTNAME=	blast+

        

          
            

              4
              
PORTVERSION=	2.5.0


              4
              
PORTVERSION=	2.7.1

            

            

              5
              
PORTREVISION=	2


              
              
            

        

          6
          
CATEGORIES=	biology

          5
          
CATEGORIES=	biology

        

        

          7
          
MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \

          6
          
MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \

        

        

          8
          
		http://acadix.biz/Ports/distfiles/

          7
          
		http://acadix.biz/Ports/distfiles/

        

  

    
      
            Lines 15-21
          
      
      
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          15
          
LICENSE=	PD

          14
          
LICENSE=	PD

        

        

          16
          
LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE

          15
          
LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE

        

        

          17
          

          16
          

        

          
            

              18
              
LIB_DEPENDS=	libpcre.so:devel/pcre


              17
              
LIB_DEPENDS=	libpcre.so:devel/pcre \

            

            

              
              

              18
              
		liblmdb.so:databases/lmdb

            

        

          19
          
RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils

          19
          
RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils

        

        

          20
          

          20
          

        

        

          21
          
WRKSRC=		${WRKDIR}/${DISTNAME}/c++

          21
          
WRKSRC=		${WRKDIR}/${DISTNAME}/c++

        



(-)distinfo
      (-3 / +3 lines)




  

    
      
            Lines 1-3
          
      
      
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              1
              
TIMESTAMP = 1480648908


              1
              
TIMESTAMP = 1518995346

            

            

              2
              
SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54


              2
              
SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca

            

            

              3
              
SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544


              3
              
SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824

            



(-)files/patch-src_build-system_Makefile.in.top
      (-11 lines)




  

    
      
            Lines 1-11
          
      
      
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              1
              
--- src/build-system/Makefile.in.top.orig	2014-11-13 01:41:55.000000000 +0900

              
              
            

            

              2
              
+++ src/build-system/Makefile.in.top	2016-12-02 16:39:58.415910000 +0900

            

            

              3
              
@@ -51,7 +51,7 @@

            

            

              4
              
 	    done

            

            

              5
              
 	cd $(includedir0) && find * -name CVS -prune -o -print |\

            

            

              6
              
             cpio -pd $(pincludedir)

            

            

              7
              
-	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)

            

            

              8
              
+	cd $(incdir) && find * | cpio -pd $(pincludedir)

            

            

              9
              
 ## set up appropriate build and status directories somewhere under $(libdir)?

            

            

              10
              
 

            

            

              11
              
 install-gbench:

            



(-)files/patch-src_build-system_configure
      (-5 / +5 lines)




  

    
      
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              1
              
--- src/build-system/configure.orig	2016-09-09 21:04:16.000000000 +0900


              1
              
--- src/build-system/configure.orig	2018-02-19 01:32:40 UTC

            

            

              2
              
+++ src/build-system/configure	2016-12-02 15:04:04.258800000 +0900


              2
              
+++ src/build-system/configure

            

            

              3
              
@@ -1715,7 +1715,7 @@


              3
              
@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do

            

            

              4
              
       | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \


              
              
            

            

              5
              
       | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \


            

        

          6
          
       | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \

          4
          
       | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \

        

            

              
              
              5
              
       | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \

            

            

              6
              
       | --datadir=* | --sysconfdir=* | --localstatedir=* \

            

        

          7
          
-      | --with-runpath=* | --with-relative-runpath=* \

          7
          
-      | --with-runpath=* | --with-relative-runpath=* \

        

        

          8
          
+      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \

          8
          
+      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \

        

        

          9
          
       | --with-experimental=* | --with-extra-action=* | --with-build-root=* \

          9
          
       | --with-experimental=* | --with-extra-action=* | --with-build-root=* \

        



(-)pkg-plist
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            Lines 10-15
          
      
      
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          10
          
bin/datatool

          10
          
bin/datatool

        

        

          11
          
bin/deltablast

          11
          
bin/deltablast

        

        

          12
          
bin/dustmasker

          12
          
bin/dustmasker

        

            

              
              
              13
              
bin/gc_cli

            

        

          13
          
bin/gene_info_reader

          14
          
bin/gene_info_reader

        

        

          14
          
bin/legacy_blast.pl

          15
          
bin/legacy_blast.pl

        

        

          15
          
bin/makeblastdb

          16
          
bin/makeblastdb

        

  

    
      
            Lines 45-50
          
      
      
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          45
          
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp

          46
          
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp

        

        

          46
          
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp

          47
          
include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp

        

        

          47
          
include/ncbi-tools++/algo/blast/api/blast_types.hpp

          48
          
include/ncbi-tools++/algo/blast/api/blast_types.hpp

        

            

              
              
              49
              
include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp

            

        

          48
          
include/ncbi-tools++/algo/blast/api/blastx_options.hpp

          50
          
include/ncbi-tools++/algo/blast/api/blastx_options.hpp

        

        

          49
          
include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp

          51
          
include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp

        

        

          50
          
include/ncbi-tools++/algo/blast/api/deltablast.hpp

          52
          
include/ncbi-tools++/algo/blast/api/deltablast.hpp

        

  

    
      
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          105
          
include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp

          107
          
include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp

        

        

          106
          
include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp

          108
          
include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp

        

        

          107
          
include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp

          109
          
include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp

        

            

              
              
              110
              
include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp

            

        

          108
          
include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp

          111
          
include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp

        

        

          109
          
include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp

          112
          
include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp

        

        

          110
          
include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp

          113
          
include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp

        

  

    
      
            Lines 175-180
          
      
      
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          175
          
include/ncbi-tools++/algo/blast/core/phi_extend.h

          178
          
include/ncbi-tools++/algo/blast/core/phi_extend.h

        

        

          176
          
include/ncbi-tools++/algo/blast/core/phi_gapalign.h

          179
          
include/ncbi-tools++/algo/blast/core/phi_gapalign.h

        

        

          177
          
include/ncbi-tools++/algo/blast/core/phi_lookup.h

          180
          
include/ncbi-tools++/algo/blast/core/phi_lookup.h

        

            

              
              
              181
              
include/ncbi-tools++/algo/blast/core/spliced_hits.h

            

        

          178
          
include/ncbi-tools++/algo/blast/core/split_query.h

          182
          
include/ncbi-tools++/algo/blast/core/split_query.h

        

        

          179
          
include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp

          183
          
include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp

        

        

          180
          
include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp

          184
          
include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp

        

  

    
      
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          181
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp

          185
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp

        

        

          182
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp

          186
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp

        

        

          183
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp

          187
          
include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp

        

            

              
              
              188
              
include/ncbi-tools++/algo/blast/format/blast_async_format.hpp

            

        

          184
          
include/ncbi-tools++/algo/blast/format/blast_format.hpp

          189
          
include/ncbi-tools++/algo/blast/format/blast_format.hpp

        

        

          185
          
include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp

          190
          
include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp

        

        

          186
          
include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp

          191
          
include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp

        

  

    
      
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          191
          
include/ncbi-tools++/algo/blast/format/sam.hpp

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include/ncbi-tools++/algo/blast/format/sam.hpp

        

        

          192
          
include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp

          197
          
include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp

        

        

          193
          
include/ncbi-tools++/algo/blast/igblast/igblast.hpp

          198
          
include/ncbi-tools++/algo/blast/igblast/igblast.hpp

        

            

              
              
              199
              
include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp

            

            

              200
              
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp

            

            

              201
              
include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp

            

            

              202
              
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp

            

            

              203
              
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp

            

            

              204
              
include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp

            

            

              205
              
include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp

            

        

          194
          
include/ncbi-tools++/algo/dustmask/sdust.tex

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include/ncbi-tools++/algo/dustmask/sdust.tex

        

        

          195
          
include/ncbi-tools++/algo/dustmask/symdust.hpp

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include/ncbi-tools++/algo/dustmask/symdust.hpp

        

        

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include/ncbi-tools++/algo/segmask/segmask.hpp

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include/ncbi-tools++/algo/segmask/segmask.hpp

        

  

    
      
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          284
          
include/ncbi-tools++/connect/ncbi_host_info.h

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include/ncbi-tools++/connect/ncbi_host_info.h

        

        

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include/ncbi-tools++/connect/ncbi_http_connector.h

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include/ncbi-tools++/connect/ncbi_http_connector.h

        

        

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include/ncbi-tools++/connect/ncbi_http_session.hpp

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include/ncbi-tools++/connect/ncbi_http_session.hpp

        

            

              
              
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include/ncbi-tools++/connect/ncbi_iprange.h

            

            

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include/ncbi-tools++/connect/ncbi_ipv6.h

            

        

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include/ncbi-tools++/connect/ncbi_lbos.hpp

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include/ncbi-tools++/connect/ncbi_lbos.hpp

        

            

              
              
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include/ncbi-tools++/connect/ncbi_localip.h

            

            

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include/ncbi-tools++/connect/ncbi_mbedtls.h

            

        

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include/ncbi-tools++/connect/ncbi_memory_connector.h

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include/ncbi-tools++/connect/ncbi_memory_connector.h

        

        

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include/ncbi-tools++/connect/ncbi_misc.hpp

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include/ncbi-tools++/connect/ncbi_misc.hpp

        

        

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include/ncbi-tools++/connect/ncbi_monkey.hpp

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include/ncbi-tools++/connect/ncbi_monkey.hpp

        

  

    
      
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include/ncbi-tools++/connect/ncbi_socket_connector.h

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include/ncbi-tools++/connect/ncbi_socket_connector.h

        

        

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include/ncbi-tools++/connect/ncbi_socket_unix.h

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include/ncbi-tools++/connect/ncbi_socket_unix.h

        

        

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include/ncbi-tools++/connect/ncbi_socket_unix.hpp

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include/ncbi-tools++/connect/ncbi_socket_unix.hpp

        

            

              
              
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include/ncbi-tools++/connect/ncbi_tls.h

            

        

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include/ncbi-tools++/connect/ncbi_types.h

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include/ncbi-tools++/connect/ncbi_types.h

        

        

          305
          
include/ncbi-tools++/connect/ncbi_userhost.hpp

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include/ncbi-tools++/connect/ncbi_userhost.hpp

        

        

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include/ncbi-tools++/connect/ncbi_util.h

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include/ncbi-tools++/connect/ncbi_util.h

        

  

    
      
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          327
          
include/ncbi-tools++/connect/services/netcache_api.hpp

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include/ncbi-tools++/connect/services/netcache_api.hpp

        

        

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include/ncbi-tools++/connect/services/netcache_api_expt.hpp

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include/ncbi-tools++/connect/services/netcache_api_expt.hpp

        

        

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include/ncbi-tools++/connect/services/netcache_key.hpp

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include/ncbi-tools++/connect/services/netcache_key.hpp

        

            

              
              
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include/ncbi-tools++/connect/services/netcache_search.hpp

            

        

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include/ncbi-tools++/connect/services/netcomponent.hpp

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include/ncbi-tools++/connect/services/netcomponent.hpp

        

        

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include/ncbi-tools++/connect/services/neticache_client.hpp

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include/ncbi-tools++/connect/services/neticache_client.hpp

        

        

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include/ncbi-tools++/connect/services/netschedule_api.hpp

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include/ncbi-tools++/connect/services/netschedule_api.hpp

        

  

    
      
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include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp

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include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp

        

        

          338
          
include/ncbi-tools++/connect/services/netstorage.hpp

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include/ncbi-tools++/connect/services/netstorage.hpp

        

        

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include/ncbi-tools++/connect/services/netstorage_ft.hpp

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include/ncbi-tools++/connect/services/netstorage_ft.hpp

        

            

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include/ncbi-tools++/connect/services/netstorage_impl.hpp

              
              
            

        

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include/ncbi-tools++/connect/services/ns_client_factory.hpp

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include/ncbi-tools++/connect/services/ns_client_factory.hpp

        

        

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include/ncbi-tools++/connect/services/ns_job_serializer.hpp

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include/ncbi-tools++/connect/services/ns_job_serializer.hpp

        

        

          343
          
include/ncbi-tools++/connect/services/ns_output_parser.hpp

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include/ncbi-tools++/connect/services/ns_output_parser.hpp

        

  

    
      
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          446
          
include/ncbi-tools++/corelib/rwstream.hpp

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include/ncbi-tools++/corelib/rwstream.hpp

        

        

          447
          
include/ncbi-tools++/corelib/stream_utils.hpp

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include/ncbi-tools++/corelib/stream_utils.hpp

        

        

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include/ncbi-tools++/corelib/syslog.hpp

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include/ncbi-tools++/corelib/syslog.hpp

        

            

              
              
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include/ncbi-tools++/corelib/teamcity_messages.h

            

        

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include/ncbi-tools++/corelib/tempstr.hpp

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include/ncbi-tools++/corelib/tempstr.hpp

        

        

          450
          
include/ncbi-tools++/corelib/test_boost.hpp

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include/ncbi-tools++/corelib/test_boost.hpp

        

        

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include/ncbi-tools++/corelib/test_mt.hpp

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include/ncbi-tools++/corelib/test_mt.hpp

        

        

          452
          
include/ncbi-tools++/corelib/version.hpp

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include/ncbi-tools++/corelib/version.hpp

        

            

              
              
              471
              
include/ncbi-tools++/db/error_codes.hpp

            

            

              472
              
include/ncbi-tools++/db/sqlite/sqlitewrapp.hpp

            

        

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include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp

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include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp

        

        

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include/ncbi-tools++/dbapi/dbapi.hpp

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include/ncbi-tools++/dbapi/dbapi.hpp

        

        

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include/ncbi-tools++/dbapi/dbapi_variant_convert.hpp

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include/ncbi-tools++/dbapi/dbapi_variant_convert.hpp

        

  

    
      
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include/ncbi-tools++/html/writer_htmlenc.hpp

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include/ncbi-tools++/html/writer_htmlenc.hpp

        

        

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include/ncbi-tools++/misc/error_codes.hpp

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include/ncbi-tools++/misc/error_codes.hpp

        

        

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include/ncbi-tools++/ncbi_pch.hpp

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include/ncbi-tools++/ncbi_pch.hpp

        

            

              
              
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include/ncbi-tools++/ncbi_random_macro.h

            

        

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include/ncbi-tools++/ncbi_source_ver.h

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include/ncbi-tools++/ncbi_source_ver.h

        

        

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include/ncbi-tools++/ncbiconf.h

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include/ncbi-tools++/ncbiconf.h

        

        

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include/ncbi-tools++/ncbiconf_unix.h

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include/ncbi-tools++/ncbiconf_unix.h

        

  

    
      
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include/ncbi-tools++/objects/seq/seq_macros.hpp

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include/ncbi-tools++/objects/seq/seq_macros.hpp

        

        

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include/ncbi-tools++/objects/seq/seqlocinfo.hpp

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include/ncbi-tools++/objects/seq/seqlocinfo.hpp

        

        

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include/ncbi-tools++/objects/seq/seqport_util.hpp

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include/ncbi-tools++/objects/seq/seqport_util.hpp

        

            

              
              
              2446
              
include/ncbi-tools++/objects/seq/so_map.hpp

            

        

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include/ncbi-tools++/objects/seq/sofa_map.hpp

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include/ncbi-tools++/objects/seq/sofa_map.hpp

        

        

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include/ncbi-tools++/objects/seq/sofa_type.hpp

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include/ncbi-tools++/objects/seq/sofa_type.hpp

        

        

          2427
          
include/ncbi-tools++/objects/seqalign/.cvsignore

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include/ncbi-tools++/objects/seqalign/.cvsignore

        

  

    
      
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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp

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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp

        

        

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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp

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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp

        

        

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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp

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include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp

        

            

              
              
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include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply.hpp

            

            

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include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply_.hpp

            

            

              3001
              
include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest.hpp

            

            

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include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest_.hpp

            

        

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include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp

          3003
          
include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp

        

        

          2978
          
include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp

          3004
          
include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp

        

        

          2979
          
include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp

          3005
          
include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp

        

  

    
      
            Lines 3012-3017
          
      
      
        Link Here
      
    
  

        

          3012
          
include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp

          3038
          
include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp

        

        

          3013
          
include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp

          3039
          
include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp

        

        

          3014
          
include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp

          3040
          
include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp

        

            

              
              
              3041
              
include/ncbi-tools++/objects/trackmgr/primary_snp.hpp

            

        

          3015
          
include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp

          3042
          
include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp

        

        

          3016
          
include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp

          3043
          
include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp

        

        

          3017
          
include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp

          3044
          
include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp

        

  

    
      
            Lines 3237-3244
          
      
      
        Link Here
      
    
  

        

          3237
          
include/ncbi-tools++/objmgr/table_field.hpp

          3264
          
include/ncbi-tools++/objmgr/table_field.hpp

        

        

          3238
          
include/ncbi-tools++/objmgr/tse_handle.hpp

          3265
          
include/ncbi-tools++/objmgr/tse_handle.hpp

        

        

          3239
          
include/ncbi-tools++/objmgr/unsupp_editsaver.hpp

          3266
          
include/ncbi-tools++/objmgr/unsupp_editsaver.hpp

        

            

              
              
              3267
              
include/ncbi-tools++/objmgr/util/autodef.hpp

            

            

              3268
              
include/ncbi-tools++/objmgr/util/autodef_available_modifier.hpp

            

            

              3269
              
include/ncbi-tools++/objmgr/util/autodef_feature_clause.hpp

            

            

              3270
              
include/ncbi-tools++/objmgr/util/autodef_feature_clause_base.hpp

            

            

              3271
              
include/ncbi-tools++/objmgr/util/autodef_mod_combo.hpp

            

            

              3272
              
include/ncbi-tools++/objmgr/util/autodef_options.hpp

            

            

              3273
              
include/ncbi-tools++/objmgr/util/autodef_source_desc.hpp

            

            

              3274
              
include/ncbi-tools++/objmgr/util/autodef_source_group.hpp

            

        

          3240
          
include/ncbi-tools++/objmgr/util/create_defline.hpp

          3275
          
include/ncbi-tools++/objmgr/util/create_defline.hpp

        

        

          3241
          
include/ncbi-tools++/objmgr/util/feature.hpp

          3276
          
include/ncbi-tools++/objmgr/util/feature.hpp

        

            

              
              
              3277
              
include/ncbi-tools++/objmgr/util/feature_edit.hpp

            

            

              3278
              
include/ncbi-tools++/objmgr/util/indexer.hpp

            

        

          3242
          
include/ncbi-tools++/objmgr/util/obj_sniff.hpp

          3279
          
include/ncbi-tools++/objmgr/util/obj_sniff.hpp

        

        

          3243
          
include/ncbi-tools++/objmgr/util/objutil.hpp

          3280
          
include/ncbi-tools++/objmgr/util/objutil.hpp

        

        

          3244
          
include/ncbi-tools++/objmgr/util/seq_align_util.hpp

          3281
          
include/ncbi-tools++/objmgr/util/seq_align_util.hpp

        

  

    
      
            Lines 3290-3295
          
      
      
        Link Here
      
    
  

        

          3290
          
include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_formatter.hpp

          3327
          
include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_formatter.hpp

        

        

          3291
          
include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp

          3328
          
include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp

        

        

          3292
          
include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp

          3329
          
include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp

        

            

              
              
              3330
              
include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp

            

        

          3293
          
include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp

          3331
          
include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp

        

        

          3294
          
include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp

          3332
          
include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp

        

        

          3295
          
include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp

          3333
          
include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp

        

  

    
      
            Lines 3372-3384
          
      
      
        Link Here
      
    
  

        

          3372
          
include/ncbi-tools++/objtools/data_loaders/loaders.hpp

          3410
          
include/ncbi-tools++/objtools/data_loaders/loaders.hpp

        

        

          3373
          
include/ncbi-tools++/objtools/edit/apply_object.hpp

          3411
          
include/ncbi-tools++/objtools/edit/apply_object.hpp

        

        

          3374
          
include/ncbi-tools++/objtools/edit/autodef.hpp

          3412
          
include/ncbi-tools++/objtools/edit/autodef.hpp

        

            

              3375
              
include/ncbi-tools++/objtools/edit/autodef_available_modifier.hpp

              
              
            

            

              3376
              
include/ncbi-tools++/objtools/edit/autodef_feature_clause.hpp

            

            

              3377
              
include/ncbi-tools++/objtools/edit/autodef_feature_clause_base.hpp

            

            

              3378
              
include/ncbi-tools++/objtools/edit/autodef_mod_combo.hpp

            

        

          3379
          
include/ncbi-tools++/objtools/edit/autodef_options.hpp

          3413
          
include/ncbi-tools++/objtools/edit/autodef_options.hpp

        

        

          3380
          
include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp

          3414
          
include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp

        

          
            

              3381
              
include/ncbi-tools++/objtools/edit/autodef_source_group.hpp


              3415
              
include/ncbi-tools++/objtools/edit/autodef_with_tax.hpp

            

        

          3382
          
include/ncbi-tools++/objtools/edit/capitalization_string.hpp

          3416
          
include/ncbi-tools++/objtools/edit/capitalization_string.hpp

        

        

          3383
          
include/ncbi-tools++/objtools/edit/cds_fix.hpp

          3417
          
include/ncbi-tools++/objtools/edit/cds_fix.hpp

        

        

          3384
          
include/ncbi-tools++/objtools/edit/dblink_field.hpp

          3418
          
include/ncbi-tools++/objtools/edit/dblink_field.hpp

        

  

    
      
            Lines 3385-3390
          
      
      
        Link Here
      
    
  

        

          3385
          
include/ncbi-tools++/objtools/edit/edit_exception.hpp

          3419
          
include/ncbi-tools++/objtools/edit/edit_exception.hpp

        

        

          3386
          
include/ncbi-tools++/objtools/edit/feattable_edit.hpp

          3420
          
include/ncbi-tools++/objtools/edit/feattable_edit.hpp

        

        

          3387
          
include/ncbi-tools++/objtools/edit/field_handler.hpp

          3421
          
include/ncbi-tools++/objtools/edit/field_handler.hpp

        

            

              
              
              3422
              
include/ncbi-tools++/objtools/edit/gap_trim.hpp

            

        

          3388
          
include/ncbi-tools++/objtools/edit/gaps_edit.hpp

          3423
          
include/ncbi-tools++/objtools/edit/gaps_edit.hpp

        

        

          3389
          
include/ncbi-tools++/objtools/edit/gb_block_field.hpp

          3424
          
include/ncbi-tools++/objtools/edit/gb_block_field.hpp

        

        

          3390
          
include/ncbi-tools++/objtools/edit/gene_utils.hpp

          3425
          
include/ncbi-tools++/objtools/edit/gene_utils.hpp

        

  

    
      
            Lines 3420-3428
          
      
      
        Link Here
      
    
  

        

          3420
          
include/ncbi-tools++/objtools/format/gbseq_formatter.hpp

          3455
          
include/ncbi-tools++/objtools/format/gbseq_formatter.hpp

        

        

          3421
          
include/ncbi-tools++/objtools/format/genbank_formatter.hpp

          3456
          
include/ncbi-tools++/objtools/format/genbank_formatter.hpp

        

        

          3422
          
include/ncbi-tools++/objtools/format/genbank_gather.hpp

          3457
          
include/ncbi-tools++/objtools/format/genbank_gather.hpp

        

            

              3423
              
include/ncbi-tools++/objtools/format/gff3_formatter.hpp

              
              
            

            

              3424
              
include/ncbi-tools++/objtools/format/gff_formatter.hpp

            

            

              3425
              
include/ncbi-tools++/objtools/format/gff_gather.hpp

            

        

          3426
          
include/ncbi-tools++/objtools/format/item_formatter.hpp

          3458
          
include/ncbi-tools++/objtools/format/item_formatter.hpp

        

        

          3427
          
include/ncbi-tools++/objtools/format/item_ostream.hpp

          3459
          
include/ncbi-tools++/objtools/format/item_ostream.hpp

        

        

          3428
          
include/ncbi-tools++/objtools/format/items/accession_item.hpp

          3460
          
include/ncbi-tools++/objtools/format/items/accession_item.hpp

        

  

    
      
            Lines 3470-3475
          
      
      
        Link Here
      
    
  

        

          3470
          
include/ncbi-tools++/objtools/readers/error_container.hpp

          3502
          
include/ncbi-tools++/objtools/readers/error_container.hpp

        

        

          3471
          
include/ncbi-tools++/objtools/readers/fasta.hpp

          3503
          
include/ncbi-tools++/objtools/readers/fasta.hpp

        

        

          3472
          
include/ncbi-tools++/objtools/readers/fasta_exception.hpp

          3504
          
include/ncbi-tools++/objtools/readers/fasta_exception.hpp

        

            

              
              
              3505
              
include/ncbi-tools++/objtools/readers/fasta_reader_utils.hpp

            

        

          3473
          
include/ncbi-tools++/objtools/readers/featuredump.hpp

          3506
          
include/ncbi-tools++/objtools/readers/featuredump.hpp

        

        

          3474
          
include/ncbi-tools++/objtools/readers/format_guess_ex.hpp

          3507
          
include/ncbi-tools++/objtools/readers/format_guess_ex.hpp

        

        

          3475
          
include/ncbi-tools++/objtools/readers/getfeature.hpp

          3508
          
include/ncbi-tools++/objtools/readers/getfeature.hpp

        

  

    
      
            Lines 3495-3500
          
      
      
        Link Here
      
    
  

        

          3495
          
include/ncbi-tools++/objtools/readers/rm_reader.hpp

          3528
          
include/ncbi-tools++/objtools/readers/rm_reader.hpp

        

        

          3496
          
include/ncbi-tools++/objtools/readers/source_mod_parser.hpp

          3529
          
include/ncbi-tools++/objtools/readers/source_mod_parser.hpp

        

        

          3497
          
include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp

          3530
          
include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp

        

            

              
              
              3531
              
include/ncbi-tools++/objtools/readers/struct_cmt_reader.hpp

            

        

          3498
          
include/ncbi-tools++/objtools/readers/table_filter.hpp

          3532
          
include/ncbi-tools++/objtools/readers/table_filter.hpp

        

        

          3499
          
include/ncbi-tools++/objtools/readers/track_data.hpp

          3533
          
include/ncbi-tools++/objtools/readers/track_data.hpp

        

        

          3500
          
include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp

          3534
          
include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp

        

  

    
      
            Lines 3624-3629
          
      
      
        Link Here
      
    
  

        

          3624
          
include/ncbi-tools++/util/bitset/bmgamma.h

          3658
          
include/ncbi-tools++/util/bitset/bmgamma.h

        

        

          3625
          
include/ncbi-tools++/util/bitset/bmrandom.h

          3659
          
include/ncbi-tools++/util/bitset/bmrandom.h

        

        

          3626
          
include/ncbi-tools++/util/bitset/bmserial.h

          3660
          
include/ncbi-tools++/util/bitset/bmserial.h

        

            

              
              
              3661
              
include/ncbi-tools++/util/bitset/bmsparsevec.h

            

            

              3662
              
include/ncbi-tools++/util/bitset/bmsparsevec_algo.h

            

            

              3663
              
include/ncbi-tools++/util/bitset/bmsparsevec_serial.h

            

        

          3627
          
include/ncbi-tools++/util/bitset/bmsse2.h

          3664
          
include/ncbi-tools++/util/bitset/bmsse2.h

        

        

          3628
          
include/ncbi-tools++/util/bitset/bmsse4.h

          3665
          
include/ncbi-tools++/util/bitset/bmsse4.h

        

        

          3629
          
include/ncbi-tools++/util/bitset/bmsse_util.h

          3666
          
include/ncbi-tools++/util/bitset/bmsse_util.h

        

  

    
      
            Lines 3709-3714
          
      
      
        Link Here
      
    
  

        

          3709
          
include/ncbi-tools++/util/resize_iter.hpp

          3746
          
include/ncbi-tools++/util/resize_iter.hpp

        

        

          3710
          
include/ncbi-tools++/util/resource_pool.hpp

          3747
          
include/ncbi-tools++/util/resource_pool.hpp

        

        

          3711
          
include/ncbi-tools++/util/retry_ctx.hpp

          3748
          
include/ncbi-tools++/util/retry_ctx.hpp

        

            

              
              
              3749
              
include/ncbi-tools++/util/row_reader.hpp

            

            

              3750
              
include/ncbi-tools++/util/row_reader.inl

            

            

              3751
              
include/ncbi-tools++/util/row_reader_base.hpp

            

            

              3752
              
include/ncbi-tools++/util/row_reader_char_delimited.hpp

            

            

              3753
              
include/ncbi-tools++/util/row_reader_excel_csv.hpp

            

            

              3754
              
include/ncbi-tools++/util/row_reader_iana_csv.hpp

            

            

              3755
              
include/ncbi-tools++/util/row_reader_iana_tsv.hpp

            

            

              3756
              
include/ncbi-tools++/util/row_reader_ncbi_tsv.hpp

            

        

          3712
          
include/ncbi-tools++/util/scheduler.hpp

          3757
          
include/ncbi-tools++/util/scheduler.hpp

        

        

          3713
          
include/ncbi-tools++/util/sequtil/sequtil.hpp

          3758
          
include/ncbi-tools++/util/sequtil/sequtil.hpp

        

        

          3714
          
include/ncbi-tools++/util/sequtil/sequtil_convert.hpp

          3759
          
include/ncbi-tools++/util/sequtil/sequtil_convert.hpp

        

  

    
      
            Lines 3887-3892
          
      
      
        Link Here
      
    
  

        

          3887
          
lib/libpcsubstance.a

          3932
          
lib/libpcsubstance.a

        

        

          3888
          
lib/libproj-static.a

          3933
          
lib/libproj-static.a

        

        

          3889
          
lib/libproj.a

          3934
          
lib/libproj.a

        

            

              
              
              3935
              
lib/libproteinkmer-static.a

            

            

              3936
              
lib/libproteinkmer.a

            

        

          3890
          
lib/libpub-static.a

          3937
          
lib/libpub-static.a

        

        

          3891
          
lib/libpub.a

          3938
          
lib/libpub.a

        

        

          3892
          
lib/libpubmed-static.a

          3939
          
lib/libpubmed-static.a

        






  

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